[2024-01-24 14:21:50,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,460] [INFO] DQC Reference Directory: /var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference
[2024-01-24 14:21:51,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:51,834] [INFO] Task started: Prodigal
[2024-01-24 14:21:51,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg4534af41-e24b-4a58-ae44-d1fcb825a741/GCF_019139795.1_ASM1913979v1_genomic.fna.gz | prodigal -d GCF_019139795.1_ASM1913979v1_genomic.fna/cds.fna -a GCF_019139795.1_ASM1913979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:16,019] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:16,019] [INFO] Task started: HMMsearch
[2024-01-24 14:22:16,020] [INFO] Running command: hmmsearch --tblout GCF_019139795.1_ASM1913979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference/reference_markers.hmm GCF_019139795.1_ASM1913979v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:16,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:16,374] [INFO] Found 6/6 markers.
[2024-01-24 14:22:16,428] [INFO] Query marker FASTA was written to GCF_019139795.1_ASM1913979v1_genomic.fna/markers.fasta
[2024-01-24 14:22:16,429] [INFO] Task started: Blastn
[2024-01-24 14:22:16,429] [INFO] Running command: blastn -query GCF_019139795.1_ASM1913979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference/reference_markers.fasta -out GCF_019139795.1_ASM1913979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:17,377] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:17,381] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:17,382] [INFO] Target genome list was writen to GCF_019139795.1_ASM1913979v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:17,393] [INFO] Task started: fastANI
[2024-01-24 14:22:17,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg4534af41-e24b-4a58-ae44-d1fcb825a741/GCF_019139795.1_ASM1913979v1_genomic.fna.gz --refList GCF_019139795.1_ASM1913979v1_genomic.fna/target_genomes.txt --output GCF_019139795.1_ASM1913979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:42,627] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:42,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:42,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:42,648] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:42,648] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:22:42,648] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	100.0	2075	2076	95	inconclusive
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	95.7803	1822	2076	95	inconclusive
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	92.4407	1745	2076	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	92.2425	1743	2076	95	below_threshold
Pseudomonas vancouverensis	strain=Dha-51	GCA_004348895.1	95300	95300	type	True	87.7746	1544	2076	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	87.7574	1550	2076	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.6801	1545	2076	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.6729	1520	2076	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.4209	1479	2076	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.4093	1480	2076	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	87.3238	1537	2076	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.4113	1409	2076	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.2037	1397	2076	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.6486	1393	2076	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.2919	854	2076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:42,650] [INFO] DFAST Taxonomy check result was written to GCF_019139795.1_ASM1913979v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:42,650] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:42,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:42,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference/checkm_data
[2024-01-24 14:22:42,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:42,711] [INFO] Task started: CheckM
[2024-01-24 14:22:42,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019139795.1_ASM1913979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019139795.1_ASM1913979v1_genomic.fna/checkm_input GCF_019139795.1_ASM1913979v1_genomic.fna/checkm_result
[2024-01-24 14:23:52,457] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:52,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:52,486] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:52,487] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:52,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019139795.1_ASM1913979v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:52,488] [INFO] Task started: Blastn
[2024-01-24 14:23:52,488] [INFO] Running command: blastn -query GCF_019139795.1_ASM1913979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg918cca05-527a-4ac5-9a68-bb399e883d3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019139795.1_ASM1913979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:54,372] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:54,376] [INFO] Selected 14 target genomes.
[2024-01-24 14:23:54,376] [INFO] Target genome list was writen to GCF_019139795.1_ASM1913979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:54,386] [INFO] Task started: fastANI
[2024-01-24 14:23:54,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg4534af41-e24b-4a58-ae44-d1fcb825a741/GCF_019139795.1_ASM1913979v1_genomic.fna.gz --refList GCF_019139795.1_ASM1913979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019139795.1_ASM1913979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:21,131] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:21,149] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:21,149] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002934665.1	s__Pseudomonas_E laurylsulfatiphila	95.7811	1821	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.74	0.86	0.82	13	conclusive
GCF_000282455.1	s__Pseudomonas_E sp000282455	92.8023	1627	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	92.5044	1673	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_003053605.1	s__Pseudomonas_E sp003053605	92.473	1714	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_902498135.1	s__Pseudomonas_E fluorescens_BH	92.4611	1705	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_002236115.1	s__Pseudomonas_E jessenii	92.4407	1745	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_002906155.1	s__Pseudomonas_E laurylsulfativorans	92.2477	1743	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002303925.1	s__Pseudomonas_E sp002303925	92.2109	1675	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_016909445.1	s__Pseudomonas_E stutzeri_A	92.1107	1657	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
GCF_003050925.1	s__Pseudomonas_E sp003050925	91.9913	1656	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.23	96.92	0.93	0.89	3	-
GCF_002113025.1	s__Pseudomonas_E sp002113025	91.9141	1652	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.31	95.23	0.87	0.84	4	-
GCF_002113375.1	s__Pseudomonas_E sp002113375	91.4618	1661	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348895.1	s__Pseudomonas_E vancouverensis	87.7813	1543	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002356535.2	s__Pseudomonas_E sp002356535	87.5782	1572	2076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.89	96.62	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:21,151] [INFO] GTDB search result was written to GCF_019139795.1_ASM1913979v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:21,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:21,155] [INFO] DFAST_QC result json was written to GCF_019139795.1_ASM1913979v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:21,156] [INFO] DFAST_QC completed!
[2024-01-24 14:24:21,156] [INFO] Total running time: 0h2m31s